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Fixed many issues regarding to compilation with C++ and compilation in
2010-06-27
David
v
an der Spo
e
l
F
ixe
d
many issues regardi
n
g
to
compilation with C+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David
van der Spoel
Fixed Makefil
e
.
am
leading t
o
warni
n
gs
.
commit
|
commitdiff
|
tree
2010-06-14
Davi
d
van der Spoel
Fixed make_edi
.
c
commit
|
commitdiff
|
tree
2010-06-14
David van der
S
poel
Merge branch 'master'
o
f
gi
t
.
gromacs
.
o
r
g:gromac
s
commit
|
commitdiff
|
tree
2010-06-14
David van
d
er
S
p
oel
Added more
f
ixes in
c
omment te
x
ts, gene
r
ously
p
rovid
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
D
avid v
a
n der Spoel
Fixed a l
o
t of spe
l
ling errors in co
m
ments and
d
ocumentation
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
D
avid van der Spoel
Merge bran
c
h 'maste
r
' of
g
it
.
gr
o
macs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-06-11
David
v
an d
e
r Spoel
Fixed force
f
i
e
ld f
i
les for ATP in orde
r
to clear bug
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Merge b
r
anch 'maste
r
' of git
.
gromacs
.
o
r
g:groma
c
s
commit
|
commitdiff
|
tree
2010-06-10
Da
v
id van der
Spoel
Made le
g
end more or less work in g_chi
.
D
on't
k
now
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
v
an d
e
r Spoel
Fi
x
e
d
SEGV i
n
g_chi as
descri
b
ed in bug 430
.
commit
|
commitdiff
|
tree
2010-06-10
David
v
an der
Spoel
Added
o
ption
-
nopbc to g_rmsdist in order to fix
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
van der Spoel
Pedantic c
h
ange in th
e
c
heck whether a filename is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
van der Spoel
Renamed s
o
me programs to
follow th
e
g_ doctrine:
l
uck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Spoel
Clean
e
d
up
and renamed files
i
n ngm
x
director
y
to be
t
ter
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van der Sp
o
el
Re
n
a
med some file
s
in a
r
oundabout way to adhe
r
e
to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Da
v
i
d van der Spoel
Removed av
e
rage
.
c,
th
a
t
fu
n
ctionality is now
i
n g_analyze
.
commit
|
commitdiff
|
tree
2010-06-10
D
a
v
id van der Spoel
Fi
x
ed strange typo in gmx_di
h
.
c
commit
|
commitdiff
|
tree
2010-06-06
Davi
d
van
d
er Spoel
Moved warning m
e
ssage in add_atomty
p
e
t
o be
p
r
i
n
ted
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
David
v
a
n der Spoel
Made x2top (very) s
l
i
gh
t
l
y funct
i
onal again
.
S
t
i
ll
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
v
i
d
v
a
n der Spoel
Changed erro
r
message for settl
e
probl
e
ms, such
t
hat
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van
d
er Spoel
Added explicit ang
l
e in ACE declarat
i
on in
gr
o
mac
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Dav
i
d
v
a
n
der S
p
oel
Fixed type
i
n gm
x
_morph
.
c: efT
R
O ->
efTRX which le
a
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David
v
a
n
d
er Spoel
Fixe
d
b
u
g
3
96
.
In f
a
ct i
t
was already fixed p
a
r
tl
y
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoel
Fixed b
u
g
401 by
i
mplementing
t
h
e proposed patch that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
avid van
d
er Spoel
Fixed bug 381 by adding the
n
u
m
ber of the
first atom
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der
Spoel
Fixed
bug 349
.
The file made with the -vis option has
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoe
l
M
e
rge branch 'ma
s
ter
'
of git
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-06-02
D
avid van der Spoel
Removed
option CAN_DT from g
_
ms
d
,
s
ince i
t
cannot handle
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Dav
i
d van
d
er Sp
o
el
Increased
buffer
s
ize
fo
r
reading in a wh
o
le f
i
le at
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
Dav
i
d van der
Spoel
Mer
g
e b
r
a
nch
'
m
a
ster' of git
.
gromac
s
.
or
g
:gro
m
acs
commit
|
commitdiff
|
tree
2010-05-25
David van der Spoel
Added one more!
commit
|
commitdiff
|
tree
2010-05-24
David v
a
n der
Spoel
Removed C++ s
t
yle comme
n
t
s in
mdrun
.
commit
|
commitdiff
|
tree
2010-05-21
David van der Spoe
l
Fixed compilation
w
arnings and re
m
oved spurio
u
s C+
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
D
avid van d
e
r
S
p
o
e
l
Added 1
commit
|
commitdiff
|
tree
2010-05-20
David va
n
d
er
S
p
oel
Made g_analyze co
m
p
ile
agai
n
, but
ot link yet
.
commit
|
commitdiff
|
tree
2010-05-19
Dav
i
d
van der Spoel
Merge branch 'master' of
g
it
.
grom
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-19
David van der Spoel
Added check in read_p
d
b for existence of
t
_res
i
nfo
.
.
.
commit
|
commitdiff
|
tree
2010-05-18
David
van der
S
p
o
e
l
A
d
ded
a
cool q
u
ote, an
d
rem
o
ved two comma's in openmp
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
Dav
i
d van der Spoel
Merge branch 'master' of
git
.
g
r
omacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-05-16
David van der Spoel
F
ixed sc
a
ttering funct
i
on code in g_rdf
.
A new file
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David
v
a
n der Spoel
Adde
d
mult
i
r
e
gre
s
sion analysis to g
_
a
n
a
l
yz
e
.
See info
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David va
n
der Spoel
Fi
x
ed
c
ompilation issue
in geminate
.
c due to n
o
n-de
f
ine
d
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David
v
an der Spoel
Mer
g
e
branch 'master'
o
f gi
t
@
git
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-05-12
David
v
an der Spo
e
l
M
erge bran
c
h 'maste
r
'
o
f git
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-05-12
D
a
v
id van de
r
Spoel
Delte
d
two mo
r
e
superflu
o
us f
i
le
s
commit
|
commitdiff
|
tree
2010-05-11
David van d
e
r
S
po
e
l
C
l
eaned up in
t
o
p directory
.
Moved a few
old
i
tp files
.
.
.
commit
|
commitdiff
|
tree
2010-05-11
D
a
v
i
d
van der Spoel
Moved phosphate files int
o
gm
x
.
ff directory
.
commit
|
commitdiff
|
tree
2010-05-11
David v
a
n der
Spoel
Moved p
r
opanol itp fi
l
e
t
op oplsaa
.
ff,
r
emoved two
.
.
.
commit
|
commitdiff
|
tree
2010-05-02
David
v
an der Spoel
Merge branch
'master' of gi
t
@git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-04-30
David van der Spoel
Added
o
ne
commit
|
commitdiff
|
tree
2010-04-26
David van
d
e
r Spo
e
l
Mad
e
histogra
m
ming slightly m
o
re
f
lexibl
e
.
Use
d
in
.
.
.
commit
|
commitdiff
|
tree
2010-04-12
Dav
i
d va
n
der Spoel
M
e
rge
b
ranch '
m
as
t
er' of gi
t
@git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-04-12
David va
n
der Spoel
Ch
a
nged the o
u
t
p
ut of topology files to i
n
c
lude the
.
.
.
commit
|
commitdiff
|
tree
2010-04-06
David van
d
er Spo
e
l
Merge
br
a
nc
h
'
m
ast
e
r' of git@git
.
groma
c
s
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-04-06
David
v
an
d
er
S
poel
Added statement to
s
e
t
rt
p
to NULL
.
commit
|
commitdiff
|
tree
2010-04-06
David va
n
der Spoel
Revert "Added argu
m
ent
rtpname
t
o
t_a
t
oms_set_resi
n
fo
.
.
.
commit
|
commitdiff
|
tree
2010-04-06
David van der S
p
oe
l
Ad
d
ed argumen
t
rtpname to t_atoms_set_
r
esi
n
fo
to av
o
id
.
.
.
commit
|
commitdiff
|
tree
2010-04-04
David va
n
d
er Spoel
A
d
ded
o
ne
.
commit
|
commitdiff
|
tree
2010-04-04
David v
a
n
d
er Spoel
Merge branch 'm
a
ste
r
' of gi
t
.
gro
m
acs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-03-31
Dav
i
d
van der
Spoel
Added one
commit
|
commitdiff
|
tree
2010-03-12
David van de
r
S
p
oel
M
erge
b
ranch 'maste
r
' of git
.
gromac
s
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-03-12
David van der
Spoel
Added
f
lush after writing to debug file
commit
|
commitdiff
|
tree
2010-03-11
David
van der Spoel
A
d
ed
f
unction copy_t_atoms
,
updated fu
n
c
t
ion ad
d
_
t
_
a
toms
.
.
.
commit
|
commitdiff
|
tree
2010-03-10
David va
n
der
S
poe
l
M
erge branch
'master' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-03-10
D
a
vid van der
S
poel
Added routine
add_t_atoms
t
o
i
ncrease the
l
ength of
.
.
.
commit
|
commitdiff
|
tree
2010-02-15
David van
d
er Spoel
Updat
e
d
commit
|
commitdiff
|
tree
2010-02-14
David van der S
p
oel
Added fun
c
tio
n
to increase the
array
s
i
zes in a t_atoms
.
.
.
commit
|
commitdiff
|
tree
2010-02-13
Da
v
id
van der S
p
oe
l
R
e
placed
s
ome strc
p
y by strncpy to av
o
id overflows
.
commit
|
commitdiff
|
tree
2010-02-09
David van
der Spoel
M
e
rge branc
h
'
mas
t
er'
of git@g
i
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-02-09
D
a
v
i
d van de
r
Sp
o
el
Added an empty
line to sha
r
e/ht
m
l
/Makefi
l
e
.
am
to fo
o
l
.
.
.
commit
|
commitdiff
|
tree
2010-02-06
David van der Spoel
F
ixed htmldir stuff
.
commit
|
commitdiff
|
tree
2010-02-06
David van der Spoel
Re
p
laced two strcpy by strnc
p
y in pdbi
o
.
c to
prevent
.
.
.
commit
|
commitdiff
|
tree
2010-02-05
Dav
i
d van der Spoe
l
Configure now u
s
e
s
the --htmldir
o
ption
.
commit
|
commitdiff
|
tree
2010-02-05
David van der Spoe
l
Con
f
igure n
o
w u
s
e
s
the --htmldir option
.
commit
|
commitdiff
|
tree
2010-02-05
Da
v
id van d
e
r Spo
e
l
Me
r
ge b
r
anch
'maste
r
' of
git
.
gromacs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-02-03
D
a
vid van der Spoel
Re
m
oved FF
.
dat from share
/
top/
M
a
k
e
fi
l
e
.
am
commit
|
commitdiff
|
tree
2010-02-01
D
a
vid
v
an der Spoel
M
e
r
g
e branch 'm
a
s
ter' of
g
it
.
g
r
omacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-01-31
David van der Spoel
Merge branch 'mas
t
er'
of g
i
t@git
.
g
r
omacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-01-31
David van der Spoel
A
d
d
ed f
i
l
e
type
.
c
u
b
for Gaussian cube
f
iles
.
commit
|
commitdiff
|
tree
2010-01-28
David van der Spoel
Merge bra
n
ch 'm
a
ster'
of
g
it@gi
t
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-01-28
Davi
d
van der Spoel
Added -ncons
t
r option to g_e
n
er
g
y in order t
o
g
e
t
c
orrect
.
.
.
commit
|
commitdiff
|
tree
2010-01-28
Da
v
id van
de
r
S
p
oel
Re
n
amed func
t
i
o
n
in ca
l
l to low_gmxl
i
bfn
commit
|
commitdiff
|
tree
2010-01-28
David van der Spoel
Added 1
.
commit
|
commitdiff
|
tree
2010-01-27
David va
n
der Spoel
No
w
I'v
e
added all
the Makefile
.
am for th
e
fo
r
ce
f
ields
.
commit
|
commitdiff
|
tree
2010-01-27
D
avid van der Spoel
Fixed Makefile
.
am in shar
e
/top
.
Will a
d
d th
e
M
ak
e
file
.
.
.
commit
|
commitdiff
|
tree
2010-01-26
D
avid van der S
p
o
e
l
Merge branch 'mas
t
er'
o
f git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-01-26
D
a
vid
v
an der
Spo
e
l
c
l
arified comment
ab
o
ut water
o
ptimization
commit
|
commitdiff
|
tree
2010-01-23
David van d
e
r
S
poe
l
Added a
quote
.
commit
|
commitdiff
|
tree
2010-01-22
David
v
an d
e
r Spoel
Merge b
r
anch 'mast
e
r' of git@git
.
gromacs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-01-22
David van d
e
r Spoel
Added missing initiati
o
n st
a
tements in atompro
p
f
ollowing
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
D
a
v
id van der Spoel
M
er
g
e b
r
anch 'ma
s
t
er' of git@gi
t
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-01-22
Da
v
i
d
van de
r
Spoel
Fixe
d
atomprop
s
uch that it (again) only reads the
.
.
.
commit
|
commitdiff
|
tree
2010-01-21
Davi
d
van der
S
poel
Fi
x
ed comment for g_energy -h as well
.
commit
|
commitdiff
|
tree
2010-01-21
David van der Spoel
F
ixed
e
r
ro
n
eous
im
p
lementation of
c
alculation
of
Cp
.
.
.
commit
|
commitdiff
|
tree
2010-01-21
David
v
an der Spoel
Ma
d
e progra
m
s less verbose
about ato
m
pro
p
s and
a
bout
.
.
.
commit
|
commitdiff
|
tree
2010-01-21
David
van der Spoel
Fixed help output in g_energy
s
uch tha
t
the fluctu
a
tion
.
.
.
commit
|
commitdiff
|
tree
2010-01-21
David
van d
e
r Spoel
Merge branch
'
master' of git@g
i
t
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-01-21
David van de
r
Spoel
Add
e
d proper fluctuation o
u
tput to g_energy
.
N
o
w we
.
.
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2010-01-21
Da
v
id van der
S
p
oel
M
erge br
a
nch '
m
a
s
ter'
o
f git@git
.
gromac
s
.
org:gro
m
a
c
s
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